| Name | phconvert JSON |
| Version |
0.9.1
JSON |
| download |
| home_page | None |
| Summary | Convert Beker&Hickl, PicoQuant and other formats to Photon-HDF5. |
| upload_time | 2024-05-24 13:14:51 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.6 |
| license | The MIT License (MIT) Copyright (c) 2015-2016 The Regents of the University of California, Antonino Ingargiola and contributors. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
single-molecule fret
smfret
biophysics
file-format
hdf5
photon-hdf5
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
|
| coveralls test coverage |
No coveralls.
|
[](https://ci.appveyor.com/project/tritemio/phconvert/branch/master)
[](https://github.com/Photon-HDF5/phconvert/actions)
# phconvert
*phconvert* is a python 2 & 3 library that helps writing valid
<a href="http://photon-hdf5.org/" target="_blank">Photon-HDF5</a>
files, a file format for time stamp-based single-molecule spectroscopy.
Additionally, *phconvert* can convert to Photon-HDF5 all the common binary
formats used in solution-based single-molecule spectroscopy. These includes
PicoQuant's .HT3/.PT3/.PTU/.T3R, Becker & Hickl's .SPC/.SET and the .SM format
used by WeissLab and others for µs-ALEX smFRET.
For questions or issues running this software please use the
[Photon-HDF5 Google Group](https://groups.google.com/forum/#!forum/photon-hdf5)
or open an [issue on GitHub](https://github.com/Photon-HDF5/phconvert/issues).
- [Phconvert Documentation](https://phconvert.readthedocs.io)
## What's new
**Nov. 2018:** Phconvert 0.9 released, see the [release notes](https://github.com/Photon-HDF5/phconvert/releases/tag/0.9).
## Quick-start: Converting files to Photon-HDF5
Converting one of the supported files formats to Photon-HDF5 does not require
being able to program in python. All you need is running the "notebook"
corresponding to the file format you want to convert from, and follow the instructions therein.
For demonstration purposes, we provide [a demo service](http://photon-hdf5.github.io/Photon-HDF5-Converter)
to run the notebooks online without any installation.
With this online service, you can convert data files up to 35MB to Photon-HDF5.
To launch the demo click on the following button
(see also [instructions](http://photon-hdf5.github.io/Photon-HDF5-Converter/)):
[](http://mybinder.org/repo/Photon-HDF5/Photon-HDF5-Converter)
To execute the phconvert notebooks on your machine, you need to install the *Jupyter Notebook App* first.
A quick-start guide on installing and running the *Jupyter Notebook App* is available here:
- <a href="http://jupyter-notebook-beginner-guide.readthedocs.org/" target="_blank">Jupyter/IPython Notebook Quick Start Guide</a>
Next, you need to install the *phconvert* library with the following command
(type it in *Terminal* on OS X or Linux, or in the `cmd` prompt on Windows):
conda install -c conda-forge phconvert
Finally, you can download one of the provided notebooks and run it on your machine.
Simply, download the
[phconvert zip](https://github.com/Photon-HDF5/phconvert/archive/master.zip),
which contains all the notebooks in the `notebooks` subfolder.
### For questions or issues:
- [Open an GitHub issue](https://github.com/Photon-HDF5/phconvert/issues) or
- Ask a question on the [Photon-HDF5 Google Group](https://groups.google.com/forum/#!forum/photon-hdf5).
## Project details
### What's inside?
*phconvert* repository contains a python package (library) and a set of
[notebooks](https://github.com/Photon-HDF5/phconvert/tree/master/notebooks)
([online viewer](http://nbviewer.ipython.org/github/Photon-HDF5/phconvert/tree/master/notebooks/)).
Each notebook can convert a different format to Photon-HDF5 using the phconvert library.
If you have a file format that is not yet supported, please [open an new Issue](https://github.com/Photon-HDF5/phconvert/issues).
We are willing add support for as many file formats as possible!
### Why phconvert?
When writing Photon-HDF5 files, phconvert saves you time
and protects you against common errors that risk
to make the file not a valid Photon-HDF5. Also a description
is automatically added to each Photon-HDF5 field.
The descriptions are extracted from a [JSON file](https://github.com/Photon-HDF5/phconvert/blob/master/phconvert/specs/photon-hdf5_specs.json)
which contains the list Photon-HDF5 field names, types, and descriptions.
See also [Writing Photon-HDF5 files](http://photon-hdf5.readthedocs.org/en/latest/writing.html)
in the Photon-HDF5 reference documentation.
## Read Photon-HDF5 files
In case you just want to read Photon-HDF5 files you don't need to use phconvert.
Photon-HDF5 files can be directly opened with a standard HDF5 viewer
[HDFView](https://www.hdfgroup.org/products/java/hdfview/).
See also [Reading Photon-HDF5 files](http://photon-hdf5.readthedocs.org/en/latest/reading.html)
in the Photon-HDF5 reference documentation.
## Installation
The recommended way to install *phconvert* is using conda:
conda install -c conda-forge phconvert
If you don't have conda installed, please install the free python distribution
[Anaconda](https://store.continuum.io/cshop/anaconda/) choosing the python 3
version.
Starting from version 0.9, the aging python 2.7 is not supported anymore.
Alternatively, you can install *phconvert* in any python installation using PIP:
pip install phconvert
In this latter case, make sure that numpy and pytables are installed.
See also:
- [phconvert Release Notes](https://github.com/Photon-HDF5/phconvert/releases/).
## Dependencies
- python 3.4 or greater (3.6+ recommended)
- numpy >=1.9
- pytables >=3.1
- numba (optional) *for faster PicoQuant files decoding*
> **Note**
> when installing via `conda` all the dependencies are automatically installed.
## The phconvert library documentation (for developers)
The *phconvert* API documentation can be found on ReadTheDocs:
- [phconvert's documentation](http://phconvert.readthedocs.org/)
## License
*phconvert* is released under the open source [MIT license](https://raw.githubusercontent.com/Photon-HDF5/phconvert/master/LICENSE.txt).
## Contributing
As with other Photon-HDF5 subprojects, we encourage contributions
in any form, from simple suggestions, typo fix to the addition of new features.
Please use GitHub by opening Issues or sending Pull Requests.
All the contributors will be acknowledged in this website, and will included
as authors in the next software-paper publication.
For more details see our [contribution policy](http://photon-hdf5.readthedocs.org/en/latest/contributing.html).
## Authors & Contributors
List of contributors:
- Antonino Ingargiola (@tritemio) <tritemio AT gmail.com>
- Ted Laurence (@talaurence) <laurence2 AT llnl.gov>
- Marco Lamperti (@lampo808) <marco.lampo AT gmail.com>
- Xavier Michalet (@smXplorer) <michalet AT chem.ucla.edu>
- Anders Barth (@AndersBarth) <anders.barth AT gmail.com>
- Biswajit Pradhan (@biswajitSM) <biswajitp145 AT gmail.com.
- Sébastien Weber (@seb5g) <sebastien.weber AT cemes.fr>
- David Palmer (@dmopalmer)
We thank also @ncodina for providing PTU files and helping in testing
the PTU decoder in phconvert.
## Acknowledgements
This work was supported by NIH Grant R01-GM95904.
Release 0.9 was supported by Prof. Eitan Lerner.
Raw data
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"description": "[](https://ci.appveyor.com/project/tritemio/phconvert/branch/master)\n[](https://github.com/Photon-HDF5/phconvert/actions)\n\n# phconvert\n\n*phconvert* is a python 2 & 3 library that helps writing valid\n<a href=\"http://photon-hdf5.org/\" target=\"_blank\">Photon-HDF5</a>\nfiles, a file format for time stamp-based single-molecule spectroscopy.\nAdditionally, *phconvert* can convert to Photon-HDF5 all the common binary\nformats used in solution-based single-molecule spectroscopy. These includes\nPicoQuant's .HT3/.PT3/.PTU/.T3R, Becker & Hickl's .SPC/.SET and the .SM format\nused by WeissLab and others for \u00b5s-ALEX smFRET.\n\nFor questions or issues running this software please use the\n[Photon-HDF5 Google Group](https://groups.google.com/forum/#!forum/photon-hdf5)\nor open an [issue on GitHub](https://github.com/Photon-HDF5/phconvert/issues).\n\n- [Phconvert Documentation](https://phconvert.readthedocs.io)\n\n## What's new\n\n**Nov. 2018:** Phconvert 0.9 released, see the [release notes](https://github.com/Photon-HDF5/phconvert/releases/tag/0.9).\n\n\n## Quick-start: Converting files to Photon-HDF5\n\nConverting one of the supported files formats to Photon-HDF5 does not require\nbeing able to program in python. All you need is running the \"notebook\"\ncorresponding to the file format you want to convert from, and follow the instructions therein.\n\nFor demonstration purposes, we provide [a demo service](http://photon-hdf5.github.io/Photon-HDF5-Converter)\nto run the notebooks online without any installation.\nWith this online service, you can convert data files up to 35MB to Photon-HDF5.\nTo launch the demo click on the following button\n(see also [instructions](http://photon-hdf5.github.io/Photon-HDF5-Converter/)):\n\n[](http://mybinder.org/repo/Photon-HDF5/Photon-HDF5-Converter)\n\nTo execute the phconvert notebooks on your machine, you need to install the *Jupyter Notebook App* first.\nA quick-start guide on installing and running the *Jupyter Notebook App* is available here:\n\n- <a href=\"http://jupyter-notebook-beginner-guide.readthedocs.org/\" target=\"_blank\">Jupyter/IPython Notebook Quick Start Guide</a>\n\nNext, you need to install the *phconvert* library with the following command\n(type it in *Terminal* on OS X or Linux, or in the `cmd` prompt on Windows):\n\n conda install -c conda-forge phconvert\n\nFinally, you can download one of the provided notebooks and run it on your machine.\nSimply, download the\n[phconvert zip](https://github.com/Photon-HDF5/phconvert/archive/master.zip),\nwhich contains all the notebooks in the `notebooks` subfolder.\n\n### For questions or issues:\n\n- [Open an GitHub issue](https://github.com/Photon-HDF5/phconvert/issues) or\n- Ask a question on the [Photon-HDF5 Google Group](https://groups.google.com/forum/#!forum/photon-hdf5).\n\n\n## Project details\n\n### What's inside?\n\n*phconvert* repository contains a python package (library) and a set of\n[notebooks](https://github.com/Photon-HDF5/phconvert/tree/master/notebooks)\n([online viewer](http://nbviewer.ipython.org/github/Photon-HDF5/phconvert/tree/master/notebooks/)).\nEach notebook can convert a different format to Photon-HDF5 using the phconvert library.\n\nIf you have a file format that is not yet supported, please [open an new Issue](https://github.com/Photon-HDF5/phconvert/issues).\nWe are willing add support for as many file formats as possible!\n\n### Why phconvert?\n\nWhen writing Photon-HDF5 files, phconvert saves you time\nand protects you against common errors that risk\nto make the file not a valid Photon-HDF5. Also a description\nis automatically added to each Photon-HDF5 field.\nThe descriptions are extracted from a [JSON file](https://github.com/Photon-HDF5/phconvert/blob/master/phconvert/specs/photon-hdf5_specs.json)\nwhich contains the list Photon-HDF5 field names, types, and descriptions.\n\nSee also [Writing Photon-HDF5 files](http://photon-hdf5.readthedocs.org/en/latest/writing.html)\nin the Photon-HDF5 reference documentation.\n\n## Read Photon-HDF5 files\n\nIn case you just want to read Photon-HDF5 files you don't need to use phconvert.\nPhoton-HDF5 files can be directly opened with a standard HDF5 viewer\n[HDFView](https://www.hdfgroup.org/products/java/hdfview/).\n\nSee also [Reading Photon-HDF5 files](http://photon-hdf5.readthedocs.org/en/latest/reading.html)\nin the Photon-HDF5 reference documentation.\n\n## Installation\n\nThe recommended way to install *phconvert* is using conda:\n\n conda install -c conda-forge phconvert\n\nIf you don't have conda installed, please install the free python distribution\n[Anaconda](https://store.continuum.io/cshop/anaconda/) choosing the python 3\nversion.\nStarting from version 0.9, the aging python 2.7 is not supported anymore.\n\nAlternatively, you can install *phconvert* in any python installation using PIP:\n\n pip install phconvert\n\nIn this latter case, make sure that numpy and pytables are installed.\n\nSee also:\n\n- [phconvert Release Notes](https://github.com/Photon-HDF5/phconvert/releases/).\n\n## Dependencies\n\n- python 3.4 or greater (3.6+ recommended)\n- numpy >=1.9\n- pytables >=3.1\n- numba (optional) *for faster PicoQuant files decoding*\n\n> **Note**\n> when installing via `conda` all the dependencies are automatically installed.\n\n\n## The phconvert library documentation (for developers)\n\nThe *phconvert* API documentation can be found on ReadTheDocs:\n\n- [phconvert's documentation](http://phconvert.readthedocs.org/)\n\n## License\n\n*phconvert* is released under the open source [MIT license](https://raw.githubusercontent.com/Photon-HDF5/phconvert/master/LICENSE.txt).\n\n## Contributing\n\nAs with other Photon-HDF5 subprojects, we encourage contributions\nin any form, from simple suggestions, typo fix to the addition of new features.\nPlease use GitHub by opening Issues or sending Pull Requests.\n\nAll the contributors will be acknowledged in this website, and will included\nas authors in the next software-paper publication.\n\nFor more details see our [contribution policy](http://photon-hdf5.readthedocs.org/en/latest/contributing.html).\n\n## Authors & Contributors\n\nList of contributors:\n\n- Antonino Ingargiola (@tritemio) <tritemio AT gmail.com>\n- Ted Laurence (@talaurence) <laurence2 AT llnl.gov>\n- Marco Lamperti (@lampo808) <marco.lampo AT gmail.com>\n- Xavier Michalet (@smXplorer) <michalet AT chem.ucla.edu>\n- Anders Barth (@AndersBarth) <anders.barth AT gmail.com>\n- Biswajit Pradhan (@biswajitSM) <biswajitp145 AT gmail.com.\n- S\u00e9bastien Weber (@seb5g) <sebastien.weber AT cemes.fr>\n- David Palmer (@dmopalmer)\n\nWe thank also @ncodina for providing PTU files and helping in testing\nthe PTU decoder in phconvert.\n\n## Acknowledgements\nThis work was supported by NIH Grant R01-GM95904.\n\nRelease 0.9 was supported by Prof. Eitan Lerner.\n",
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